3KBJ

Room temperature X-ray structure of apo-D-Xylose Isomerase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.729040mg/ml protein, 30%(v/v) ammonium sulfate (sat.), pH 7.7, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.7755.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.04α = 90
b = 99.52β = 90
c = 102.47γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293IMAGE PLATERIGAKU RAXIS IV++2009-02-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODE1.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
121090321432899942
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0799.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONAB INITIOFREE R21032143160098.90.18650.18370.2262RANDOM
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
Coordinate Error
Structure Solution MethodRefinement High ResolutionRefinement Low Resolution
13263.5
RMS Deviations
KeyRefinement Restraint Deviation
s_similar_adp_cmpnt0.081
s_non_zero_chiral_vol0.039
s_zero_chiral_vol0.031
s_angle_d0.022
s_from_restr_planes0.0218
s_anti_bump_dis_restr0.008
s_bond_d0.006
s_similar_dist
s_rigid_bond_adp_cmpnt
s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3053
Nucleic Acid Atoms
Solvent Atoms243
Heterogen Atoms

Software

Software
Software NamePurpose
CrystalCleardata collection
SHELXmodel building
SHELXL-97refinement
CrystalCleardata reduction
CrystalCleardata scaling
SHELXphasing